Institut für Molekulare Infektionsbiologie
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Coagulase-negative staphylococci, particularly Staphylococcus epidermidis, have been recognised as an important cause of health care-associated infections due to catheterisation, and livestock-associated infections. The colonisation of indwelling medical devices is achieved by the formation of biofilms, which are large cell-clusters surrounded by an extracellular matrix. This extracellular matrix consists mainly of PIA (polysaccharide intercellular adhesin), which is encoded by the icaADBC-operon. The importance of icaADBC in clinical strains provoking severe infections initiated numerous investigations of this operon and its regulation within the last two decades. The discovery of a long transcript being located next to icaADBC, downstream of the regulator gene icaR, led to the hypothesis of a possible involvement of this transcript in the regulation of biofilm formation (Eckart, 2006). Goal of this work was to characterise this transcript, named ncRNA IcaZ, in molecular detail and to uncover its functional role in S. epidermidis.
The ~400 nt long IcaZ is specific for ica-positive S. epidermidis and is transcribed in early- and mid-exponential growth phase as primary transcript. The promotor sequence and the first nucleotides of icaZ overlap with the 3' UTR of the preceding icaR gene, whereas the terminator sequence is shared by tRNAThr-4, being located convergently to icaZ. Deletion of icaZ resulted in a macroscopic biofilm-negative phenotype with highly diminished PIA-biofilm. Biofilm composition was analysed in vitro by classical crystal violet assays and in vivo by confocal laser scanning microscopy under flow conditions to display biofilm formation in real-time. The mutant showed clear defects in initial adherence and decreased cell-cell adherence, and was therefore not able to form a proper biofilm under flow in contrast to the wildtype. Restoration of PIA upon providing icaZ complementation from plasmids revealed inconsistent results in the various mutant backgrounds.
To uncover the functional role of IcaZ, transcriptomic and proteomic analysis was carried out, providing some hints on candidate targets, but the varying biofilm phenotypes of wildtype and icaZ mutants made it difficult to identify direct IcaZ mRNA targets. Pulse expression of icaZ was then used as direct fishing method and computational target predictions were executed with candidate mRNAs from aforesaid approaches. The combined data of these analyses suggested an involvement of icaR in IcaZ-mediated biofilm control. Therefore, RNA binding assays were established for IcaZ and icaR mRNA. A positive gel shift was maintained with icaR 3' UTR and with 5'/3' icaR mRNA fusion product, whereas no gel shift was obtained with icaA mRNA. From these assays, it was assumed that IcaZ regulates icaR mRNA expression in S. epidermidis. S. aureus instead lacks ncRNA IcaZ and its icaR mRNA was shown to undergo autoregulation under so far unknown circumstances by intra- or intermolecular binding of 5' UTR and 3' UTR (Ruiz de los Mozos et al., 2013). Here, the Shine-Dalgarno sequence is blocked through 5'/3' UTR base pairing and RNase III, an endoribonuclease, degrades icaR mRNA, leading to translational blockade. In this work, icaR mRNA autoregulation was therefore analysed experimentally in S. epidermidis and results showed that this specific autoregulation does not take place in this organism. An involvement of RNase III in the degradation process could not be verified here. GFP-reporter plasmids were generated to visualise the interaction, but have to be improved for further investigations.
In conclusion, IcaZ was found to interact with icaR mRNA, thereby conceivably interfering with translation initiation of repressor IcaR, and thus to promote PIA synthesis and biofilm formation. In addition, the environmental factor ethanol was found to induce icaZ expression, while only weak or no effects were obtained with NaCl and glucose. Ethanol, actually is an ingredient of disinfectants in hospital settings and known as efficient effector for biofilm induction. As biofilm formation on medical devices is a critical factor hampering treatment of S. epidermidis infections in clinical care, the results of this thesis do not only contribute to better understanding of the complex network of biofilm regulation in staphylococci, but may also have practical relevance in the future.
Analysis of the mechanism and the regulation of histatin 5 resistance in \(Candida\) \(albicans\)
(2018)
Antimycotics such as fluconazole are frequently used to treat C. albicans infections of the oral mucosa. Prolonged treatment of the fungal infection with fluconazole pose a risk to resistance development. C. albicans can adapt to these stressful environmental changes by regulation of gene expression or by producing genetically altered variants that arise in the population. Adapted variants frequently carry activating mutations in zinc cluster transcription factors, which cause the upregulation of their target genes, including genes encoding efflux pumps that confer drug resistance. MDR1, regulated by the zinc cluster transcription factor Mrr1, as well as CDR1 and CDR2, regulated by the zinc cluster transcription factor Tac1, are well-known examples of genes encoding efflux pumps that extrude the antimycotic fluconazole from the fungal cell and thus contribute to the survival of the fungus.
In this study, it was investigated if C. albicans can develop resistance to the antimicrobial peptide histatin 5, which serves as the first line of defence in the oral cavity of the human host. Recently, it was shown that C. albicans transports histatin 5 outside of the Candia cell via the efflux pump Flu1. As efflux pumps are often regulated by zinc cluster transcription factors, the Flu1 efflux pump could also be regulated by a zinc cluster transcription factor which could in a hyperactive form upregulate the expression of the efflux pump, resulting in increased export of histatin 5 and consequently in histatin 5 resistance.
In order to find a zinc cluster transcription factor that upregulates FLU1 expression, a comprehensive library of C. albicans strains containing artificially activated forms of zinc cluster transcription factors was screened for suitable candidates. The screening was conducted on medium containing mycophenolic acid because mycophenolic acid is also a substrate of Flu1 and a strain expressing a hyperactive zinc cluster transcription factor that upregulates FLU1 expression should exhibit an easily recognisable mycophenolic acid-resistant phenotype. Further, FACS analysis, quantitative real-time RT-PCR analysis, broth microdilution assays as well as histatin 5 assays were conducted to analyse the mechanism and the regulation of histatin 5 resistance.
Several zinc cluster transcription factors caused mycophenolic acid resistance and upregulated FLU1 expression. Of those, only hyperactive Mrr1 was able to confer increased histatin 5 resistance. Finding Mrr1 to confer histatin 5 resistance was highly interesting as fluconazole-resistant strains with naturally occurring Mrr1 gain of function mutations exist, which were isolated from HIV-infected patients with oral candidiasis. These Mrr1 gain of function mutations as well as artificially activated Mrr1 cause fluconazole resistance by upregulation of the efflux pump MDR1 and other target genes. In the course of the study, it was found that expression of different naturally occurring MRR1 gain-of-function mutations in the SC5314 wild type background caused increased FLU1 expression and increased histatin 5 resistance. The same was true for fluconazole-resistant clinical isolates with Mrr1 gain of function mutations, which also caused the overexpression of FLU1. Those cells were less efficiently killed by histatin 5 dependent on Mrr1. Surprisingly, FLU1 contributed only little to histatin 5 resistance, rather, overexpression of MDR1 mainly contributed to the Mrr1-mediated histatin 5 resistance, but also additional Mrr1-target genes were involved. These target genes are yet to be uncovered. Moreover, if a link between the yet unknown Mrr1-target genes contributing to fluconazole resistance and increased histatin 5 resistance can be drawn remains to be discovered upon finding of the responsible target genes.
Collectively, this study contributes to the understanding of the impact of prolonged antifungal exposure on the interaction between host and fungus. Drug therapy can give rise to resistance evolution resulting in strains that have not only developed resistance to fluconazole but also to an innate host mechanism, which allows adaption to the host niche even in the absence of the drug.
Staphylococcus aureus ist ein grampositives Bakterium, welches häufig als kommensaler Besiedler auf der Nasen- und Rachenschleimhaut von Säugetieren vorkommt. Darüber hinaus besitzt dieser fakultativ pathogene Mikroorganismus die Fähigkeit schwer zu behandelnde Krankenhausinfektionen auszulösen. Aufgrund der weiten Verbreitung von Antibiotikaresistenzen und dem Mangel an effektiven Therapien, verursachen S. aureus Infektionen jährlich enorme Kosten für das Gesundheitssystem. S. aureus wird meist von der Nase zum primären Infektionsort übertragen, wodurch zunächst sehr häufig Wund- und Weichteilinfektionen hervor gerufen werden. Von diesem primären Infektionsort ausgehend, kann der Erreger tiefer liegende Gewebsschichten infizieren oder sich über den Blutstrom im gesamten Organismus ausbreiten. Das Spektrum an Krankheitsbildern reicht von leichten Abszessen der Haut bis zu schweren, lebensbedrohlichen Erkrankungen wie Pneumonien und akuter Sepsis.
Für die erfolgreiche Kolonisierung und Infektion des Wirtes exprimiert S. aureus eine Vielzahl unterschiedlicher Virulenzfaktoren. Die wohl größte Gruppe an Virulenzfaktoren umfasst die Proteine, die an der Immunevasion und der Umgehung von verschiedenen Abwehrstrategien des Immunsystems beteiligt sind. Das bisherige Wissen über die Interaktion von S. aureus mit dem Immunsystem des Wirtes und die zugrunde liegenden Pathogenitätsmechanismen ist bisher limitiert.
Um neue Erkenntnisse über die Interaktion von Wirt und Pathogen zu erlangen, wurden im Rahmen dieser Arbeit bislang unbekannte sekretierte und Oberflächen-assoziierte Proteine von S. aureus funktionell charakterisiert. Die Funktion der ausgewählten Proteine wurde in vitro hinsichtlich Einfluss auf Komponenten des Immunsystems, Adhäsion an Wirtsfaktoren und Invasion in eukaryotische Zellen untersucht.
Mit Hilfe der vorangegangenen in-vitro-Charakterisierung der putativen Virulenzfaktoren, konnte für die cytoplasmatische Adenylosuccinat-Synthase PurA eine neuartige Funktion identifiziert werden. PurA ist bekannt als essentielles Enzym der de novo Purin-Synthese. In dieser Arbeit wurde nun gezeigt, dass PurA zudem an der Immunevasion beteiligt ist. Durch die Bindung des humanen Faktor H des Komplementsystems schützt PurA S. aureus vor der lytischen Aktivität des Komplementsystems und verhindert die Opsonisierung des Pathogens. Basierend auf diesen Ergebnissen wurde PurA detailliert charakterisiert. In Bindungsstudien mit rekombinantem Faktor H und PurA wurde eine direkte Interaktion beider Proteine nachgewiesen, wobei Faktor H mit dem N-terminalen Bereich von PurA interagiert. Weiterhin konnte PurA durch Immunfluoreszenz und FACS-Analysen auf der Zelloberfläche nachgewiesen werden, wo es wahrscheinlich mit der Zellwand assoziiert vorliegt. Dort rekrutiert es Faktor H an die bakterielle Oberfläche und verhindert das Fortschreiten der Komplement-Kaskade und damit die Lyse des Pathogens. Aufgrund der Multifunktionalität zählt PurA somit zur Gruppe der Moonlighting Proteine.
Des Weiteren wurde die Rolle von PurA im Infektionsgeschehen in zwei unabhängigen Tiermodellen untersucht. In beiden Modellen wurde ein signifikant reduziertes Virulenzpotential der ΔpurA-Mutante beobachtet. Zukünftig soll geklärt werden, ob die verminderte Virulenz in der fehlenden Komplementevasion oder im Defekt in der Purin-Synthese begründet ist. Aufgrund der sehr starken Attenuation in allen untersuchten Infektionsmodellen sollte PurA als potentielles Target für eine Therapie von S. aureus Infektionen weiter charakterisiert werden. Im Ergebnis dieser Arbeit wurde demnach mit PurA ein neues Moonlighting Protein identifiziert, das als Inhibitor des Komplementsystems wesentlich zur Immunevasion von S. aureus beiträgt.
Für das bessere Verständnis der humoralen S. aureus-spezifischen Immunantwort, Unterschieden in der Antikörperantwort und der gebildeten Antikörperspezifitäten wurde weiterhin das während der Kolonisierung und Infektion gebildete S. aureus-spezifische Antikörperprofil untersucht. Dazu wurden Plasmen von humanen nasalen Trägern und Nicht-Trägern sowie murine Seren von infizierten Tieren untersucht. Insbesondere wurde das Pathogen-spezifische Antikörperprofil in unterschiedlichen Infektionsmodellen mit Hilfe eines Proteinarrays analysiert, der im Rahmen dieser Arbeit in einer Kooperation mit der Firma Alere Technologies (Jena, Deutschland) und universitären Forschergruppen der Universitäten Greifswald, Münster und Jena mitentwickelt wurde. Die Antikörperprofile von intramuskulär und intravenös infizierten Tieren resultierten in jeweils spezifischen Antikörperprofilen. Diese Ergebnisse deuten auf einen Zusammenhang zwischen der Art der Infektion und der gebildeten Antikörperspezifitäten hin. Wahrscheinlich beruht dies auf einer gewebespezifischen Genexpression als Anpassung an die individuellen Bedürfnisse im Wirtsorganismus. Das ausgebildete Antikörperprofil gibt somit einen Einblick in das Expressionsmuster von Virulenzfaktoren von S. aureus unter in vivo Bedingungen und trägt damit zum Verständnis der komplexen Interaktion von Pathogen und Wirt bei. Diese Untersuchungen ergänzen zudem die bisherigen Kenntnisse über die Anpassung der humoralen Immunantwort an eine asymptomatische Kolonisierung im Gegensatz zu einer akuten Infektion durch S. aureus. Darüber hinaus können die gewonnenen Ergebnisse für diagnostische Zwecke und zur Identifikation von neuen Zielstrukturen für eine Vakzin-Entwicklung genutzt werden.
Preclinical development of an immunotherapy against antibiotic-resistant Staphylococcus aureus
(2017)
The Gram-positive bacterium Staphylococcus aureus is the leading cause of nosocomial infections. In particular, diseases caused by methicillin-resistant S. aureus (MRSA) are associated with higher morbidity, mortality and medical costs due to showing resistance to several classes of established antibiotics and their ability to develop resistance mechanisms against new antibiotics rapidly. Therefore, strategies based on immunotherapy approaches have the potential to close the gap for an efficient treatment of MRSA.
In this thesis, a humanized antibody specific for the immunodominant staphylococcal antigen A (IsaA) was generated and thoroughly characterized as potential candidate for an antibody based therapy. A murine monoclonal antibody was selected for humanization based on its binding characteristics and the ability of efficient staphylococcal killing in mouse infection models. The murine antibody was humanized by CDR grafting and mouse and humanized scFv as well as scFv-Fc fragments were constructed for comparative binding studies to analyse the successful humanization. After these studies, the full antibody with the complete Fc region was constructed as isotype IgG1, IgG2 and IgG4, respectively to assess effector functions, including antibody-dependent killing of S. aureus. The biological activity of the humanized antibody designated hUK-66 was analysed in vitro with purified human PMNs and whole blood samples taken from healthy donors and patients at high risk of S. aureus infections, such as those with diabetes, end-stage renal disease, or artery occlusive disease (AOD).
Results of the in vitro studies show, that hUK-66 was effective in antibody-dependent killing of S. aureus in blood from both healthy controls and patients vulnerable to S. aureus infections. Moreover, the biological activity of hUK-66 and hUK-66 combined with a humanized anti-alpha-toxin antibody (hUK-tox) was investigated in vivo using a mouse pneumonia model. The in vivo results revealed the therapeutic efficacy of hUK-66 and the antibody combination of hUK-66 and hUK-tox to prevent staphylococcal induced pneumonia in a prophylactic set up.
Based on the experimental data, hUK-66 represents a promising candidate for an antibody-based therapy against antibiotic resistant MRSA.
High-throughput sequencing (HTS) has revolutionized bacterial genomics. Its unparalleled sensitivity has opened the door to analyzing bacterial evolution and population genomics, dispersion of mobile genetic elements (MGEs), and within-host adaptation of pathogens, such as Escherichia coli.
One of the defining characteristics of intestinal pathogenic E. coli (IPEC) pathotypes is a specific repertoire of virulence factors (VFs). Many of these IPEC VFs are used as typing markers in public health laboratories to monitor outbreaks and guide treatment options. Instead, extraintestinal pathogenic E. coli (ExPEC) isolates are genotypically diverse and harbor a varied set of VFs -- the majority of which also function as fitness factors (FFs) for gastrointestinal colonization.
The aim of this thesis was the genomic characterization of pathogenic and commensal E. coli with respect to their virulence- and antibiotic resistance-associated gene content as well as phylogenetic background. In order to conduct the comparative analyses, I created a database of E. coli VFs, ecoli_VF_collection, with a focus on ExPEC virulence-associated proteins (Leimbach, 2016b). Furthermore, I wrote a suite of scripts and pipelines, bac-genomics-scripts, that are useful for bacterial genomics (Leimbach, 2016a). This compilation includes tools for assembly and annotation as well as comparative genomics analyses, like multi-locus sequence typing (MLST), assignment of Clusters of Orthologous Groups (COG) categories, searching for protein homologs, detection of genomic regions of difference (RODs), and calculating pan-genome-wide association statistics.
Using these tools we were able to determine the prevalence of 18 autotransporters (ATs) in a large, phylogenetically heterogeneous strain panel and demonstrate that many AT proteins are not associated with E. coli pathotypes. According to multivariate analyses and statistics the distribution of AT variants is instead significantly dependent on phylogenetic lineages. As a consequence, ATs are not suitable to serve as pathotype markers (Zude et al., 2014).
During the German Shiga toxin-producing E. coli (STEC) outbreak in 2011, the largest to date, we were one of the teams capable of analyzing the genomic features of two isolates. Based on MLST and detection of orthologous proteins to known E. coli reference genomes the close phylogenetic relationship and overall genome similarity to enteroaggregative E. coli (EAEC) 55989 was revealed. In particular, we identified VFs of both STEC and EAEC pathotypes, most importantly the prophage-encoded Shiga toxin (Stx) and the pAA-type plasmid harboring aggregative adherence fimbriae. As a result, we could show that the epidemic was caused by an unusual hybrid pathotype of the O104:H4 serotype. Moreover, we detected the basis of the antibiotic multi-resistant phenotype on an extended-spectrum beta-lactamase (ESBL) plasmid through comparisons to reference plasmids. With this information we proposed an evolutionary horizontal gene transfer (HGT) model for the possible emergence of the pathogen (Brzuszkiewicz et al., 2011).
Similarly to ExPEC, E. coli isolates of bovine mastitis are genotypically and phenotypically highly diverse and many studies struggled to determine a positive association of putative VFs. Instead the general E. coli pathogen-associated molecular pattern (PAMP), lipopolysaccharide (LPS), is implicated as a deciding factor for intramammary inflammation. Nevertheless, a mammary pathogenic E. coli (MPEC) pathotype was proposed presumably encompassing strains more adapted to elicit bovine mastitis with virulence traits differentiating them from commensals.
We sequenced eight E. coli isolates from udder serous exudate and six fecal commensals (Leimbach et al., 2016). Two mastitis isolate genomes were closed to a finished-grade quality (Leimbach et al., 2015). The genomic sequence of mastitis-associated E. coli (MAEC) strain 1303 was used to elucidate the biosynthesis gene cluster of its O70 LPS O-antigen. We analyzed the phylogenetic genealogy of our strain panel plus eleven bovine-associated E. coli reference strains and found that commensal or MAEC could not be unambiguously allocated to specific phylogroups within a core genome tree of reference E. coli. A thorough gene content analysis could not identify functional convergence of either commensal or MAEC, instead both have only very few gene families enriched in either pathotype. Most importantly, gene content and ecoli_VF_collection analyses showed that no virulence determinants are significantly associated with MAEC in comparison to bovine fecal commensals, disproving the MPEC hypothesis. The genetic repertoire of bovine-associated E. coli, again, is dominated by phylogenetic background. This is also mostly the case for large virulence-associated E. coli gene cluster previously associated with mastitis. Correspondingly, MAEC are facultative and opportunistic pathogens recruited from the bovine commensal gastrointestinal microbiota (Leimbach et al., 2017). Thus, E. coli mastitis should be prevented rather than treated, as antibiotics and vaccines have not proven effective.
Although traditional E. coli pathotypes serve a purpose for diagnostics and treatment, it is clear that the current typing system is an oversimplification of E. coli's genomic plasticity. Whole genome sequencing (WGS) revealed many nuances of pathogenic E. coli, including emerging hybrid or heteropathogenic pathotypes. Diagnostic and public health microbiology need to embrace the future by implementing HTS techniques to target patient care and infection control more efficiently.
RNA-binding proteins (RBPs) have been extensively studied in eukaryotes, where they post-transcriptionally regulate many cellular events including RNA transport, translation, and stability. Experimental techniques, such as cross-linking and co-purification followed by either mass spectrometry or RNA sequencing has enabled the identification and characterization of RBPs, their conserved RNA-binding domains (RBDs), and the regulatory roles of these proteins on a genome-wide scale. These developments in quantitative, high-resolution, and high-throughput screening techniques have greatly expanded our understanding of RBPs in human and yeast cells. In contrast, our knowledge of number and potential diversity of RBPs in bacteria is comparatively poor, in part due to the technical challenges associated with existing global screening approaches developed in eukaryotes.
Genome- and proteome-wide screening approaches performed in silico may circumvent these technical issues to obtain a broad picture of the RNA interactome of bacteria and identify strong RBP candidates for more detailed experimental study. Here, I report APRICOT (“Analyzing Protein RNA Interaction by Combined Output Technique”), a computational pipeline for the sequence-based identification and characterization of candidate RNA-binding proteins encoded in the genomes of all domains of life using RBDs known from experimental studies. The pipeline identifies functional motifs in protein sequences of an input proteome using position-specific scoring matrices and hidden Markov models of all conserved domains available in the databases and then statistically score them based on a series of sequence-based features. Subsequently, APRICOT identifies putative RBPs and characterizes them according to functionally relevant structural properties. APRICOT performed better than other existing tools for the sequence-based prediction on the known RBP data sets. The applications and adaptability of the software was demonstrated on several large bacterial RBP data sets including the complete proteome of Salmonella Typhimurium strain SL1344. APRICOT reported 1068 Salmonella proteins as RBP candidates, which were subsequently categorized using the RBDs that have been reported in both eukaryotic and bacterial proteins. A set of 131 strong RBP candidates was selected for experimental confirmation and characterization of RNA-binding activity using RNA co-immunoprecipitation followed by high-throughput sequencing (RIP-Seq) experiments. Based on the relative abundance of transcripts across the RIP-Seq libraries, a catalogue of enriched genes was established for each candidate, which shows the RNA-binding potential of 90% of these proteins. Furthermore, the direct targets of few of these putative RBPs were validated by means of cross-linking and co-immunoprecipitation (CLIP) experiments.
This thesis presents the computational pipeline APRICOT for the global screening of protein primary sequences for potential RBPs in bacteria using RBD information from all kingdoms of life. Furthermore, it provides the first bio-computational resource of putative RBPs in Salmonella, which could now be further studied for their biological and regulatory roles. The command line tool and its documentation are available at https://malvikasharan.github.io/APRICOT/.
The infection of a eukaryotic host cell by a bacterial pathogen is one of the most intimate examples of cross-kingdom interactions in biology. Infection processes are highly relevant from both a basic research as well as a clinical point of view. Sophisticated mechanisms have evolved in the pathogen to manipulate the host response and vice versa host cells have developed a wide range of anti-microbial defense strategies to combat bacterial invasion and clear infections. However, it is this diversity and complexity that makes infection research so challenging to technically address as common approaches have either been optimized for bacterial or eukaryotic organisms. Instead, methods are required that are able to deal with the often dramatic discrepancy between host and pathogen with respect to various cellular properties and processes. One class of cellular macromolecules that exemplify this host-pathogen heterogeneity is given by their transcriptomes: Bacterial transcripts differ from their eukaryotic counterparts in many aspects that involve both quantitative and qualitative traits. The entity of RNA transcripts present in a cell is of paramount interest as it reflects the cell’s physiological state under the given condition. Genome-wide transcriptomic techniques such as RNA-seq have therefore been used for single-organism analyses for several years, but their applicability has been limited for infection studies.
The present work describes the establishment of a novel transcriptomic approach for infection biology which we have termed “Dual RNA-seq”. Using this technology, it was intended to shed light particularly on the contribution of non-protein-encoding transcripts to virulence, as these classes have mostly evaded previous infection studies due to the lack of suitable methods. The performance of Dual RNA-seq was evaluated in an in vitro infection model based on the important facultative intracellular pathogen Salmonella enterica serovar Typhimurium and different human cell lines. Dual RNA-seq was found to be capable of capturing all major bacterial and human transcript classes and proved reproducible. During the course of these experiments, a previously largely uncharacterized bacterial small non-coding RNA (sRNA), referred to as STnc440, was identified as one of the most strongly induced genes in intracellular Salmonella. Interestingly, while inhibition of STnc440 expression has been previously shown to cause a virulence defect in different animal models of Salmonellosis, the underlying molecular mechanisms have remained obscure. Here, classical genetics, transcriptomics and biochemical assays proposed a complex model of Salmonella gene expression control that is orchestrated by this sRNA. In particular, STnc440 was found to be involved in the regulation of multiple bacterial target mRNAs by direct base pair interaction with consequences for Salmonella virulence and implications for the host’s immune response. These findings exemplify the scope of Dual RNA-seq for the identification and characterization of novel bacterial virulence factors during host infection.
Die Forschungsergebnisse der letzten Jahre liefern immer mehr Hinweise darauf, dass eine klare Unterscheidung von Fitness- und Virulenzfaktoren in vielen Fällen, insbesondere bei extraintestinal pathogenen Escherichia coli, nicht möglich ist. So lässt sich auch bei Harnwegsinfektionen verursachenden E. coli den bakteriellen und teils stammspezifischen Faktoren oftmals nicht eindeutig eine typische Virulenz- oder Fitness-assoziierte Funktion zuordnen. Zudem werden in neueren Studien immer häufiger atypische uropathogene Isolate von E. coli beschrieben, die in ihrem „Virulenzrepertoire“ deutlich von typischen uropathogenen E. coli (UPEC) abweichen, da sie keine klassischen UPEC-Virulenzfaktoren aufweisen. In dieser Arbeit wurden daher Virulenzeigenschaften typischer als auch atypischer UPEC untersucht.
Der Effekt eines bestimmten bakteriellen Faktors auf den Wirtsorganismus wird teilweise indirekt durch sekundäre Modifikation bedingt. Dies offenbart sich beispielsweise am Autotransporterprotein AIDA-I, dessen Konformation durch posttranslationale Glykosylierung stabilisiert wird, wodurch es seine Funktionalität als Adhäsin erhält. Da bisherige Studien zum AIDA-I homologen Autotransporterprotein Antigen 43 (Ag43) auf der Analyse von künstlich glykosyliertem Protein basieren, lag ein Schwerpunkt dieser Arbeit auf der Untersuchung der natürlichen Glykosylierung von Ag43 in UPEC Stamm 536. Es zeigte sich, dass beide Ag43-Varianten von E. coli Stamm 536 natürlicherweise glykosyliert vorliegen, der Grad der Glykosylierung jedoch wesentlich geringer ausfällt als bei natürlich glykosyliertem AIDA-I. Inwieweit die natürliche Glykosylierung von Ag43 zu dessen Funktionalität beiträgt, kann erst durch die Identifizierung der für die Ag43-Glykosylierung verantwortlichen Glykosyltransferase geklärt werden.
Die in silico-Analyse des Genoms von UPEC Stamm 536 für potentielle Glykosyltransferasen von Ag43 lieferte neun Kandidatengene. Die Gene wurde teils im Wildtyp-Hintergrund, teils im rfaH-negativen Hintergrund von E. coli Stamm 536 deletiert und die Mutanten im Anschluss phänotypisch charakterisiert. Die Deletion der Kandidatengene waaF, waaG und waaQ, die für Glykosyltransferasen des LPS-Biosynthesesystems kodieren, führte zu den deutlichsten Unterschieden in Bezug auf Motilität, Curli/Zellulose-Produktion, Hämolyseaktivität und Expression von Typ 1 Fimbrien. Der Einfluss des „knock-out“ der Kandidatengene auf die Glykosylierung von Ag43 muss in weiterführenden Studien untersucht werden.
Zur Charakterisierung des uropathogenen Virulenzpotentials verschiedener E. coli Stämme in vivo hat sich in den letzten Jahren das murine Modell der aufsteigenden Harnwegsinfektion etabliert. Mit Hilfe dieses Modells wurden in der vorliegenden Arbeit sowohl spezifische Deletionsmutanten prototypischer UPEC als auch atypische E. coli Harnwegsisolate bezüglich ihrer Urovirulenz getestet und verglichen. Bei der Untersuchung der klassischen UPEC lag der Fokus auf der möglichen Urovirulenzmodulation durch die folgenden spezifischen Faktoren: dem Autotransporterprotein Ag43, dem „Response regulator“ UvrY, dem Polyketid Colibactin sowie dem Exopolysaccharid poly-β-1,6-N-Acetylglucosamin (PGA). Für Ag43 war bei der Etablierung einer Harnwegsinfektion keine eindeutige Funktion feststellbar. Es ist jedoch denkbar, dass Ag43 zur Langzeitpersistenz im Harnwegstrakt beitragen kann, was in weiteren Studien belegt werden sollte. Die Expression von UvrY in der natürlichen uvrY-Deletionsmutante UPEC Stamm 536 ließ keine Erhöhung des Urovirulenzpotentials im Mausmodell erkennen. In diesem Zusammenhang konnte allerdings gezeigt werden, dass die Expression des Genotoxins Colibactin in UPEC Stamm 536 dessen Virulenz signifikant herabsetzte. Die Untersuchungen zur Relevanz des Exopolysaccharids PGA belegen deutlich, dass PGA für die Langzeitpersistenz von E. coli im murinen Harnwegstrakt benötigt wird. Für die initiale Kolonisierung scheint PGA hingegen keine Bedeutung zu haben. Für atypische UPEC Isolate, die Charakteristika von STEC und EAEC zeigen und sich in ihrem Virulenzmuster deutlich von prototypischen UPEC unterscheiden, ließ sich im murinen Modell der aufsteigenden Harnwegsinfektion, verglichen mit dem UPEC Modellorganismus 536, ein ähnliches, teils sogar erhöhtes uropathogenes Virulenzpotential nachweisen.
Die Ergebnisse der Arbeit untermauern somit die heutige Vorstellung bezüglich der Entwicklung und Etablierung einer Harnwegsinfektion, dass verschiedene E. coli Stämme unterschiedliche (Kontroll-) Mechanismen entwickelt haben, um erfolgreich den Harnwegstrakt kolonisieren und eine Infektion auslösen zu können. Zudem weisen sie darauf hin, dass diese Fähigkeit nicht auf Isolate typischer phylogenetischer UPEC Entwicklungslinien beschränkt und auf das Vorhandensein charakteristischer UPEC Virulenzfaktoren angewiesen ist.
Nitrogen-regulated pathogenesis describes the expression of virulence attributes as direct response to the quantity and quality of an available nitrogen source. As consequence of nitrogen availability, the opportunistic human fungal pathogen Candida albicans changes its morphology and secretes aspartic proteases [SAPs], both well characterized virulence attributes. C. albicans, contrarily to its normally non-pathogenic relative Saccharomyces cerevisiae, is able to utilize proteins, which are considered as abundant and important nitrogen source within the human host. To assimilate complex proteinaceous matter, extracellular proteolysis is followed by uptake of the degradation products through dedicated peptide transporters (di-/tripeptide transporters [PTRs] and oligopeptide transporters [OPTs]). The expression of both traits is transcriptionally controlled by Stp1 - the global regulator of protein utilization - in C. albicans. The aim of the present study was to elucidate the regulation of virulence attributes of the pathogenic fungus C. albicans by nitrogen availability in more detail. Within a genome wide binding profile of Stp1, during growth with proteins, more than 600 Stp1 target genes were identified, thereby confirming its role in the usage of proteins, but also other nitrogenous compounds as nitrogen source. Moreover, the revealed targets suggest an involvement of Stp1 in the general adaption to nutrient availability as well as in the environmental stress response. With the focus on protein utilization and nitrogen-regulated pathogenesis, the regulation of the major secreted aspartic protease Sap2 - additionally one of the prime examples of allelic heterogeneity in C. albicans - was investigated in detail. Thereby, the heterogezygous SAP2 promoter helped to identify an unintended genomic alteration as the true cause of a growth defect of a C. albicans mutant. Additionally, the promoter region, which was responsible for the differential activation of the SAP2 alleles, was delimited. Furthermore, general Sap2 induction was demonstrated to be mediated by distinct cis-acting elements that are required for a high or a low activity of SAP2 expression. For the utilization of proteins as nitrogen source it is also crucial to take up the peptides that are produced by extracellular proteolysis. Therefore, the function and importance of specific peptide transporters was investigated in C. albicans mutants, unable to use peptides as nitrogen source (opt1Δ/Δ opt2Δ/Δ opt3Δ/Δ opt4Δ/Δ opt5Δ/Δ ptr2Δ/Δ ptr22Δ/Δ septuple null mutants). The overexpression of individual transporters in these mutants revealed differential substrate specificities and expanded the specificity of the OPTs to dipeptides, a completely new facet of these transporters. The peptide-uptake deficient mutants were further used to elucidate, whether indeed proteins and peptides are an important in vivo nitrogen source for C. albicans. It was found that during competitive colonization of the mouse intestine these mutants exhibited wild-type fitness, indicating that neither proteins nor peptides are primary nitrogen sources required to efficiently support growth of C. albicans in the mouse gut. Adequate availability of the preferred nitrogen source ammonium represses the utilization of proteins and other alternative nitrogen sources, but also the expression of virulence attributes, like Sap secretion and nitrogen-starvation induced filamentation. In order to discriminate, whether ammonium availability is externally sensed or determined inside the cell by C. albicans, the response to exterior ammonium concentrations of ammonium-uptake deficient mutants (mep1Δ/Δ mep2Δ/Δ null mutants) was investigated. This study showed that presence of an otherwise suppressing ammonium concentration did not inhibit Sap2 proteases secretion and arginine-induced filamentation in these mutants. Conclusively, ammonium availability is primarily determined inside the cell in order to control the expression of virulence traits. In sum, the present work contributes to the current understanding of how C. albicans regulates expression of virulence-associated traits in response to the presence of available nitrogen sources - especially proteins and peptides - in order to adapt its lifestyle within a human host.
Der Hefepilz Candida albicans gehört zu den opportunistischen Infektionserregern. Er ist Teil der natürlichen Mikroflora der Schleimhäute des Gastrointestinal- und Urogenitaltraktes des Menschen. Bei Störungen des natürlichen Gleichgewichts dieser Flora kann es zu oberflächlichen Mykosen, z. B. der oropharyngealen Candidiasis (Mundsoor), kommen. Besonders immunsupprimierte Patienten, wie AIDS-Patienten, leiden häufig unter immer wiederkehrenden Infektionen, die mitunter auch zu schwerwiegenden Infektionsverläufen, bis hin zu lebensbedrohlichen systemischen Mykosen führen können. Zur Therapie solcher Erkrankungen werden oft Ergosterolbiosyntheseinhibitoren, wie Fluconazol, eingesetzt. Besonders bei wiederkehrenden Infektionen und wiederholender Therapie ist C. albicans in der Lage, gegen diese häufig verabreichten Antimykotika Resistenzen zu entwickeln. Hierbei spielen Zink-Cluster-Transkriptionsfaktoren eine zentrale Rolle. Zink-Cluster-Proteine gehören zu einer pilzspezifischen Familie von Transkriptionsfaktoren, die ein großes Spektrum an zellulären Prozessen regulieren. Die gut charakterisierten Regulatoren Upc2, Tac1 und Mrr1 gehören zu den Zink-Cluster-Transkriptionsfaktoren, die maßgeblich zur Resistenzentwicklung von C. albicans beitragen. Upc2 kontrolliert die Expression vieler Ergosterolbiosynthesegene, besonders die von ERG11, welches für die Zielstruktur des gängigen Antimykotikums Fluconazol kodiert. Tac1 und Mrr1 hingegen regulieren die Expression von Multidrug-Effluxpumpen, den ABC-Transportern CDR1 und CDR2 bzw. dem Major Facilitator MDR1. Gain-of-function-Mutationen in diesen Transkriptionsfaktoren resultieren in einer konstitutiven Überexpression ihrer Zielgene und sind verantwortlich für die Resistenz vieler klinischer Isolate. In dieser Arbeit wurde gezeigt, dass die Fusion von Mrr1 mit der Gal4-Aktivierungsdomäne von Saccharomyces cerevisiae zu einem konstitutiv aktiven Hybridtranskriptionsfaktor führte, der eine MDR1-Überexpression bewirkte und Fluconazolresistenz vermittelte. Dieses Hybridprotein vermittelte sogar eine höhere Resistenz als ein Mrr1 mit natürlich vorkommenden gain-of-function-Mutationen. Analoge Fusionen mit Tac1 und Upc2 resultierten ebenfalls in einer konstitutiven Aktivierung dieser Transkriptionsfaktoren, die einen starken Anstieg der Fluconazolresistenz zur Folge hatte. Daraus ergab sich die Schlussfolgerung, dass dies eine generelle Methode sein könnte, die Zink-Cluster-Transkriptionsfaktoren künstlich zu aktivieren und so ihre biologischen Funktionen zu offenbaren, ohne die genauen Bedingungen für ihre Aktivität zu kennen. Deshalb wurde auf der Basis dieser Strategie eine Bibliothek von C.-albicans-Stämmen konstruiert, in der alle 82 putativen Zink-Cluster-Transkriptionsfaktoren in dieser möglicherweise hyperaktiven Form exprimiert werden. Untersuchungen dieser Bibliothek offenbarten neue Transkriptionsfaktoren, die Fluconazolresistenz vermittelten, aber auch noch unbekannte Regulatoren der Morphogenese und andere Phänotypen konnten beobachtet werden. Um einen tieferen Einblick in die Funktionsweise zu bekommen, wurden die Transkriptionsprofile der vier Transkriptionsfaktoren ermittelt, die in ihrer hyperaktiven Form die höchste Fluconazolresistenz bewirkten. Dabei stellte sich heraus, dass die zwei künstlich aktivierten (*) Regulatoren ZCF34* und ZNC1* die Expression der wichtigsten Multidrug-Effluxpumpe CDR1 stark hochregulierten. Der Transkriptionsfaktor mit dem vorläufigen Namen ZCF34 konnte im Verlauf dieser Arbeit als ein wichtiger Regulator für die CDR1-Expression identifiziert werden. Er ist sowohl an der Aktivierung der Expression von CDR1 beteiligt als auch für die basale CDR1-Promotoraktivität notwendig. Aus diesem Grund wurde er in MRR2 (multidrug resistance regulator 2) umbenannt. Mit der Entdeckung eines neuen Regulators der wichtigsten Multidrug-Effluxpumpe von C. albicans wurde ein wichtiger Beitrag zum Verständnis der Regulation solcher Transporter geleistet. Die Überexpression dieser Pumpen ist einer der häufigsten Resistenzmechanismen in C. albicans. Auf diesem Wege kann Resistenz gegen strukturell völlig unterschiedliche Antimykotika bewirkt werden. Somit stellen sowohl diese Effluxpumpen, als auch deren Regulatoren mögliche Angriffsziele für die Entwicklung neuer oder Weiterentwicklung bereits vorhandener Antimykotika dar.